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The cavefish genome reveals candidate genes for eye loss

Author

Listed:
  • Suzanne E. McGaugh

    (The Genome Institute, Washington University, Campus Box 8501
    Present address: Ecology, Evolution, and Behavior, University of Minnesota, 100 Ecology Building, 1987 Upper Buford Cir, Falcon Heights, Minnesota 55108, USA)

  • Joshua B. Gross

    (University of Cincinnati)

  • Bronwen Aken

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton
    European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton)

  • Maryline Blin

    (DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard)

  • Richard Borowsky

    (New York University)

  • Domitille Chalopin

    (Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS)

  • Hélène Hinaux

    (DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard)

  • William R. Jeffery

    (University of Maryland)

  • Alex Keene

    (University of Nevada)

  • Li Ma

    (University of Maryland)

  • Patrick Minx

    (The Genome Institute, Washington University, Campus Box 8501)

  • Daniel Murphy

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton
    European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton)

  • Kelly E. O’Quin

    (Centre College)

  • Sylvie Rétaux

    (DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard)

  • Nicolas Rohner

    (Harvard Medical School Department of Genetics)

  • Steve M. J. Searle

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton)

  • Bethany A. Stahl

    (University of Cincinnati)

  • Cliff Tabin

    (Harvard Medical School Department of Genetics)

  • Jean-Nicolas Volff

    (Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS)

  • Masato Yoshizawa

    (University of Nevada)

  • Wesley C. Warren

    (The Genome Institute, Washington University, Campus Box 8501)

Abstract

Natural populations subjected to strong environmental selection pressures offer a window into the genetic underpinnings of evolutionary change. Cavefish populations, Astyanax mexicanus (Teleostei: Characiphysi), exhibit repeated, independent evolution for a variety of traits including eye degeneration, pigment loss, increased size and number of taste buds and mechanosensory organs, and shifts in many behavioural traits. Surface and cave forms are interfertile making this system amenable to genetic interrogation; however, lack of a reference genome has hampered efforts to identify genes responsible for changes in cave forms of A. mexicanus. Here we present the first de novo genome assembly for Astyanax mexicanus cavefish, contrast repeat elements to other teleost genomes, identify candidate genes underlying quantitative trait loci (QTL), and assay these candidate genes for potential functional and expression differences. We expect the cavefish genome to advance understanding of the evolutionary process, as well as, analogous human disease including retinal dysfunction.

Suggested Citation

  • Suzanne E. McGaugh & Joshua B. Gross & Bronwen Aken & Maryline Blin & Richard Borowsky & Domitille Chalopin & Hélène Hinaux & William R. Jeffery & Alex Keene & Li Ma & Patrick Minx & Daniel Murphy & K, 2014. "The cavefish genome reveals candidate genes for eye loss," Nature Communications, Nature, vol. 5(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms6307
    DOI: 10.1038/ncomms6307
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